Have you put your son on 3 hour EASY? When we first started to correct our accidental parenting and to begin to teach independent sleep to our son at 7 weeks, we had the same problem at night (though naps were really tough in that he wouldn't sleep very long!). I'm not going to lie, it took about 4 weeks to get him to fall asleep faster. He just needs to learn how to do it and you are doing the right thing to help him out, we did the exact same thing! He would never really cry (except when he woke early from a nap and we tried to extend it) only fuss and would squirm constantly trying to break out of his swaddle, too. How long have you been working at this for? Do you turn him on his side to pat/ssh? We found this didn't work well and ended up gently patting him on his chest while he was laying on his back and holding a hand over his eyes if he was keeping them open (a sign of being overstimulated). What time does he go to bed? Our little guy was not falling asleep before 11pm when we first started and for the longest time got stuck around 8:30-9:00. As soon as we managed to move it back to 8:00 and even better 7:30, he was falling asleep much more quickly as well.
Don't give up, you are on the right track! Sometimes there are no easy answers, just hard work that will pay off in the end!
Oops! Noticed one other thing in your post that might be a problem - maybe your lo's naps are a tad too long? It depends on the A time but I'm pretty sure in the book, Tracy recommends at your lo's age to not let them sleep through a feed during the day which means, for example;
e7:00
a7:30
s8:15
and your lo takes a 2.5 hour nap, the next e would be at 10:45, almost 4 hours past the first one.....maybe waking them up a little closer to the feed may help. I think on 3 hour easy you aim for 3 1:30-1:45 naps and a cat nap.
Another thing that can make it difficult for them to fall asleep is being awake too long before bed. Having a short little nap between the second last feed and bedtime can help: ie. eat at 4, nap 5:15-6:00, bath at 6:30, feed at 7:00, to bed at 7:30.